Our goal in this study is to discover highly specific diagnostic non-invasive biomarkers by analyzing a large cohort (n=660) patient urine samples for different kidney transplant injury phenotypes in pediatric renal transplantation. Kidney transplantation is the treatment of choice for children with end stage kidney disease. Graft survival is limited by the accrual of different injuries such as acute rejection (AR), chronic allograft nephropathy (CAN), and viral infection with the BK virus (BKV), which are indistinguishable by simply monitoring the serum creatinine and require an invasive biopsy for diagnosis of established injury. Urine being an ultrafiltrate of plasma and a direct filtrate of the kidney provides a valuable resource for monitoring graft health and dysfunction. In this proposal, we propose to employ a cutting-edge, comprehensive analysis of the urinary proteome by using recently developed and LC-FT MS/MS-UStags based peptidomics analysis of native urinary peptides and LC-MS/MS based soluble protein analysis of human urine. Availability of state-of-the-art proteomics facility at PNNL and an environment of outstanding bioinformatics with available comprehensive Clinical Database at Stanford will support high-throughput biomarker screening and data analysis for selection of 20 most significant peptides and proteins for differentiating different graft injury phenotypes- AR, CAN, BKV and stable functioning grafts (STA). The selection of the most biologically relevant candidates will be aided by robust integrative proteogenomic data analysis which will use overlapping biopsy microarray data and urine proteomic data from the same patients, collected at the same time-point. Specific and sensitive non-invasive urinary biomarkers discovery for different phenotypes of graft injury will undergo pre-clinical validation by SRM on an independent set of 480 urine samples for diagnosis and prediction. The protein/peptide markers will be useful in developing ELISA assays which can be used for clinical monitoring of graft injury, replacing the invasive transplant biopsy.